Function main

src/main.cpp:168–1221

}

int main(int argc, char *argv[])
{

    print_version();

	const char* conf_file = get_conf_file(argc, argv);

	ConfigFile cf(conf_file);

	//read parameters and initial variables:

	unsigned int max_threads = (int)cf.Value("general", "maxThreads", 1);
	bool thread_verbose = (bool)cf.Value("general", "threadVerbose", "false");

	thread_init(max_threads, thread_verbose ? 1 : 0);


    std::string sex = (std::string)cf.Value("general","sex", "");
	if (sex.compare("XX") == 0) {
	  std::cout << "..consider the sample being female\n";
	} else if (sex.compare("XY") == 0) {
	  std::cout << "..consider the sample being male\n";
	} else if (sex.compare("") != 0){
	  std::cerr << "Error: \"sex\" can be either XX or XY\n";
	  return 0;
	}

	double breakPointThreshold = (double)cf.Value("general","breakPointThreshold", .8);
	if (breakPointThreshold < 0) {
	  cerr << "\n\n\t!!ERROR!! (but don't be afraid :)\n\n";
	  cerr << "Starting from FREEC v.4.2 we use the threshold on the slope of the slope of the RSSs (instead of simply slope in FREEC v.<4.1) to define number of breakpoints in segmentation. ";
	  cerr << "This method is more robust and should provide a more uniform segmentation for different chromosomes.\n";
	  cerr << "\n\tWe recomend to use \"breakPointThreshold=0.8\"\n\n";
	  cerr << "It should be a positive value. The higher it is, the less breakpoints you will get.\n";
	  cerr << "\n\tI am sorry, but you need to change this value in your config profile.. Or your can just comment it with #, then the default values of 0.8 will be applied\n";
	  return 0;
	}
	std::cout << "..Breakpoint threshold for segmentation of copy number profiles is "<< breakPointThreshold<< "\n";

    int teloCentroFlanks = (int)cf.Value("general","telocentromeric", TELO_CENTRO_FLANCS);
	std::cout << "..telocenromeric set to "<<teloCentroFlanks<<"\n";

    bool ifBedGraphOutPut = (bool)cf.Value("general","BedGraphOutput", "false");
	if (!ifBedGraphOutPut) {
	  std::cout << "..FREEC is not going to output normalized copy number profiles into a BedGraph file (for example, for visualization in the UCSC GB). Use \"[general] BedGraphOutput=TRUE\" if you want a BedGraph file\n";
	}

 	bool contaminationAdjustment = (bool)cf.Value("general","contaminationAdjustment", "false");
	if (!contaminationAdjustment) {
	  std::cout << "..FREEC is not going to adjust profiles for a possible contamination by normal cells\n";
	} else {
      std::cout << "..FREEC is going to adjust profiles for a possible contamination by normal cells\n";
      std::cout <<"..set contaminationAdjustment=FALSE if you don't want to use this option because you think that there is no contamiantion of your tumor sample by normal cells (e.g., it is a cell line, or it non-cancer DNA used without a control sample)\n";
	}
	float knownContamination = (float)cf.Value("general","contamination",0);

    if (knownContamination>0) {
            if (contaminationAdjustment == false) {